Preprocessing - Tran

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Description

This function computes the transition matrix corresponding to a specific matrix of latent states.

Usage

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Tran(xi)

Arguments

xi

Matrix of estimated latent states

Details

The matrix of latent states must consider only 4 states:

  1. Loss

  2. Neutral

  3. Gain

  4. Amplification

Value

A 4 by 4 matrix with transition probabilities derived from the input matrix of latent states.

Author(s)

Alberto Cassese

References

Guha S, Li Y, Neuberg D. Bayesian hidden Markov modelling of array cgh data. JASA. 2008;103(482):485-497.

Examples

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data(NCI_60)

X <- NCI_60$aCGH
xi <- InitXi(X)
tran <- Tran(xi)